Data and Resources
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Additional Info
| Field | Value |
|---|---|
| Title | The effect of diet and breed on global gene expression profiles of animals divergent for RFI |
| License | Licence Not Specified | Teagasc Department | Animal and Bioscience Research |
| Téama | Animal and Grassland |
| Cur síos | |
| Language | English |
| Principal Investigator (PI) | Dr David Kenny |
| Principal Investigator (PI) email | david.kenny@teagasc.ie |
| Data creator(s) |
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| Citation | Keogh K, McKenna C, Waters SM, Porter RK et al. Effect of breed and diet on the M. longissimus thoracis et lumborum transcriptome of steers divergent for residual feed intake. Sci Rep 2023 Jun 3;13(1):9034. PMID: 37270611 |
| Landing page | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113135 |
| Related resources |
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| Provenance information | Raw read quality was checked with FASTQC; adapters and low-quality reads were removed with Cutadapt. Trimmed reads were aligned to the bovine reference genome ARS-UCD1.2 with STAR (mean 90.62% mapped), and gene-level counts for protein-coding genes were generated using STAR "quantMode GeneCounts" against the Ensembl v87 annotation. Genes with <1 count per million in at least half the samples per comparison were removed; data were TMM-normalised and differential expression between H- and L-RFI steers was tested within each breed x diet comparison using exact tests in edgeR. A separate model evaluated the breed x diet interaction (RFI as class variable, animal as random effect). DEGs were defined as Benjamini-Hochberg FDR < 0.1 and fold change > 1.5 (230 DEGs across six comparisons; 23 interaction genes). DEGs were annotated and analysed for pathway enrichment using Ingenuity Pathway Analysis (Qiagen). |